Owen2011TrackingModifier.cpp

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#include "Owen2011TrackingModifier.hpp"
#include "Owen2011OxygenBasedCellCycleModel.hpp"
#include "QuiescentCancerCellMutationState.hpp"
#include "CancerCellMutationState.hpp"
#include "WildTypeCellMutationState.hpp"
#include "PottsMesh.hpp"

template<unsigned DIM>
Owen2011TrackingModifier<DIM>::Owen2011TrackingModifier()
: AbstractCellBasedSimulationModifier<DIM>()
  {
  }

template<unsigned DIM>
Owen2011TrackingModifier<DIM>::~Owen2011TrackingModifier()
{
}

template<unsigned DIM>
void Owen2011TrackingModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    UpdateCellData(rCellPopulation);
}

template<unsigned DIM>
void Owen2011TrackingModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
{
    /*
     * We must update CellData in SetupSolve(), otherwise it will not have been
     * fully initialised by the time we enter the main time loop.
     */
    UpdateCellData(rCellPopulation);
}

template<unsigned DIM>
void Owen2011TrackingModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{

    // Make sure the cell population is updated
    rCellPopulation.Update();

    // Recover each cell's concentrations from the ODEs and store in CellData
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
            cell_iter != rCellPopulation.End();
            ++cell_iter)
    {
        Owen2011OxygenBasedCellCycleModel* p_model = static_cast<Owen2011OxygenBasedCellCycleModel*>(cell_iter->GetCellCycleModel());
        double this_phi = p_model->GetPhi();
        double this_p53 = p_model->GetP53();
        double this_VEGF = p_model->GetVEGF();

        // Note that the state variables must be in the same order as listed in Owen2011OxygenBasedOdeSystem
        cell_iter->GetCellData()->SetItem("Phi", this_phi);
        cell_iter->GetCellData()->SetItem("p53", this_p53);
        cell_iter->GetCellData()->SetItem("VEGF", this_VEGF);

        // also calculate number of normal and cancerous neighbours
        unsigned number_of_normal_neighbours = 0;
        unsigned number_of_cancerous_neighbours = 0;

        std::set<unsigned> neighbouring_node_indices = static_cast<PottsMesh<DIM>& >(rCellPopulation.rGetMesh()).GetMooreNeighbouringNodeIndices(rCellPopulation.GetLocationIndexUsingCell(*cell_iter));
        std::set<unsigned>::iterator node_it;
        for (node_it = neighbouring_node_indices.begin(); node_it != neighbouring_node_indices.end(); node_it++)
        {
            if (rCellPopulation.IsCellAttachedToLocationIndex(*node_it))
            {
                std::set<CellPtr> neighbour_cells = rCellPopulation.GetCellsUsingLocationIndex(*node_it);
                std::set<CellPtr>::iterator cell_neighbour_it;
                for (cell_neighbour_it = neighbour_cells.begin(); cell_neighbour_it != neighbour_cells.end(); cell_neighbour_it++)
                {

                    if ((*cell_neighbour_it)->GetMutationState()->template IsType<WildTypeCellMutationState>())
                    {
                        number_of_normal_neighbours++;
                    }
                    if ((*cell_neighbour_it)->GetMutationState()->template IsType<CancerCellMutationState>() ||
                            (*cell_neighbour_it)->GetMutationState()->template IsType<QuiescentCancerCellMutationState>())
                    {
                        number_of_cancerous_neighbours++;
                    }

                }
            }
        }

        cell_iter->GetCellData()->SetItem("Number_of_cancerous_neighbours", number_of_cancerous_neighbours);
        cell_iter->GetCellData()->SetItem("Number_of_normal_neighbours", number_of_normal_neighbours);
    }
}

template<unsigned DIM>
void Owen2011TrackingModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    // No parameters to output, so just call method on direct parent class
    AbstractCellBasedSimulationModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}

// Explicit instantiation
template class Owen2011TrackingModifier<1>;
template class Owen2011TrackingModifier<2>;
template class Owen2011TrackingModifier<3>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(Owen2011TrackingModifier)